By checking your worktodo.txt against results.txt on a daily basis and removing k n pairs from your worktodo.txt that have already been factored and posted in results.txt.
Edit: Thanks shauge. I wrote my answer before seeing your post. I did not consider that Joh14vers6 would have used an obsolete worktoto file. Actually, even my advice to check it daily would not always work. You are correct in saying that there is no way to prevent this from happening.